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Molecular Genomics

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The Molecular Genomics Core (MGC) is a single resource for research that requires analysis of the human genome or transcriptome, the set of all RNA molecules. The MGC provides expertise and technologies for:

  • Sequence analysis
  • The design and analysis of PCR-based assays
  • The design and analysis of microarray-based assays
  • The ability to multiplex assays
  • Understanding of the organization of genes, genomes, and epigenetic factors

 The Core has instrumentation for automated sequencing, real-time quantitation of PCR-based assays, nucleic acid fragment analysis, several formats of array-based assays, and robotic liquid handlers for the automation of certain protocols.

The Molecular Genomics Core provides expertise and tools for genomic and transcriptomic analysis to Cancer Center members. Services include:

  • DNA sequencing, using Big Dye™ chemistry on the ABI3130XL capillary sequencing instrument, with automated Phred quality scoring and optional Blast searches; sequencing of plasmid, cosmid, BAC, PCR product, genomic, and bisulfite treated DNA; mitochondrial re-sequencing with Affymetrix arrays
  • SNP determination or mutational analysis, performed on individual samples/genes by single molecule sequencing, performed on multiple samples or multiple genes as a Taqman based allelic discrimination assay, performed on multiple samples and in multiple genes in a high-throughput fashion with single base extension assays using SNPstream, Infinium, or GoldenGate technology, and finally, on single samples at a whole genome level with microarray technology
  • Quantitative analysis of nucleic acid content (genes or transcripts) in individual samples with ABI 7900 real-time PCR instruments (96-well, 384-well, and Taqman platforms)
  • Array-based quantitation of whole transcriptomes, microRNA, or targeted subsets of the genome or transcriptome with multiple platforms: Affymetrix, Agilent, Exiqon, Illumina (BeadArrays), CombiMatrix, Xceed Molecular Ziplex and others
  • Comparative genome hybridization analysis
  • Experimental design services:
          o Primer design for sequencing or PCR
          o Assay design for quantitative PCR
          o Multiplexed assay design for quantitative PCR (gene expression validation), SNP determination(Taqman, SNPstream, or Illumina BeadXpress), or splice variant resolution (PCR based or array based)
         o Transcriptome analysis with gene expression arrays
         o Genome analysis for copy number variation, methylation analysis, SNP, or mutation detection
         o ChIP-on-Chip analysis of transcription factors, chromatin domains, or RNA binding proteins
  • Analysis of data from all the above experimental situations as well as:
         o Validation studies – PCR based or array based, from study data or publically available data
         o Genome alignment of findings – identifying SNPs associated with genes or genes associated with SNPs, promoters associated with genes, genes associated with copy number variations, and interspecies chromosomal alignments
         o Biological inference analysis – pathway analysis, gene ontology analysis, gene set enrichment analysis
         o Target molecule identification for cell surface markers, blood biomarkers, drug development, immune therapy, and disease association studies
          o Signature development
  • Additional services:
          o shRNA library for both mouse and human transcriptomes
          o Sample preparation information
          o Data storage with metadata annotation
          o Quality control validation of data
          o Data upload to public databases
          o Training in the unassisted use of qPCR machines and bioinformatics software for data analysis
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